OBJECTIVE To evaluate the conservation of the MHC-E locus throughout anthropoid primate evolution, we identified the homologue of the HLA-E locus in six different New World monkey species. RESULTS Full-length sequencing of MHC-E cDNAs in four unrelated cotton-top tamarins (Saguinus oedipus) revealed no evidence for polymorphism. Using the PCR, denaturing gradient gel electrophoresis, and direct sequencing, we also identified MHC-E alleles in five other New World monkey species, representing all extant platyrrhine families. In contrast to all other classical and nonclassical MHC class I genes in primates, the rate of synonymous nucleotide substitution is much greater than the rate of nonsynonymous nucleotide substitution within exons 2 and 3 encoding the peptide binding region (PBR) in MHC-E genes. DISCUSSION The PBR of the MHC-E molecule has evolved under purifying selective pressures, and the very unusual evolutionary history of this ancient gene provides further evidence that the products of the HLA-E locus serve a critical immunological function. FUTURE DIRECTIONS Given the remarkable conservation of the PBR during primate evolution, this critical immunological function is probably related to the peptide binding ability of the MHC-E protein. KEY WORDS MHC, HLA-E, New World FUNDING NIH RR00167, DK44886 PUBLICATIONS Knapp, LA, Cadavid, LF, and D.I. Watkins. 1998. The MHC-E locus is the most ancient and well-conserved of all known primate class I histocompatibility genes. J. Immunol. 160:189-196.